id summary reporter owner description type status priority milestone component version resolution keywords cc blockedby blocking notify_on_close platform project 17933 Crash on Mac waking from sleep chimerax-bug-report@… Tom Goddard "{{{ The following bug report has been submitted: Platform: macOS-15.4.1-arm64-arm-64bit ChimeraX Version: 1.9 (2024-12-11 19:11:19 UTC) Description Last time you used ChimeraX it crashed. This is a known crash that we are unable to fix. Here is information that may help you avoid this crash. The Qt window toolkit crashed due to a display configuration change, typically when waking from sleep or when an external display is disconnected or connected. This has only been seen on Mac computers. We hope a newer version of Qt will fix it. We update ChimeraX daily builds whenever a new Qt is released. You can check here https://www.cgl.ucsf.edu/chimerax/docs/troubleshoot.html#macdisplay to see if it has been fixed in a newer ChimeraX. 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All rights reserved. How to cite UCSF ChimeraX > open /Users/z.kilic/Downloads/7LFH.cif Summary of feedback from opening /Users/z.kilic/Downloads/7LFH.cif --- note | PDBx/mmCIF styling lost on line 20299. Rereading mmCIF file from the beginning. 7LFH.cif title: Cryo-EM structure of NLRP3 double-ring cage, 6-fold (12-mer) [more info...] Chain information for 7LFH.cif #1 --- Chain | Description | UniProt A B C D E F G H I J K L | NACHT,LRR and PYD domains-containing protein 3 | NLRP3_MOUSE 1-1033 > style stick Changed 76884 atom styles > style stick Changed 76884 atom styles > style sphere Changed 76884 atom styles > style sphere Changed 76884 atom styles > style ball Changed 76884 atom styles > style ball Changed 76884 atom styles > style stick Changed 76884 atom styles > show cartoons > style stick Changed 76884 atom styles > style ball Changed 76884 atom styles > style sphere Changed 76884 atom styles > style stick Changed 76884 atom styles > show atoms > hide atoms > select down Nothing selected > select ~sel & ##selected Nothing selected > select down Nothing selected > open /Users/z.kilic/Downloads/MmCPLs_fit-SCMC-PADI6_250529.cxs Opened cryosparc_P105_J56_006_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 2.12, shown at level 0.289, step 1, values float32 Opened cryosparc_P105_J67_007_volume_map_sharp.mrc as #4, grid size 300,300,300, pixel 2.12, shown at level 0.276, step 1, values float32 opened ChimeraX session > hide atoms > show #!1 models > hide #!1 models > color bychain > color byhetero > color bychain > show cartoons > volume #!4 style surface > volume #!4 style mesh > volume #!4 style image > open /Users/z.kilic/Downloads/MmCPLs_fit-SCMC-PADI6_250529.cxs Opened cryosparc_P105_J56_006_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 2.12, shown at level 0.289, step 1, values float32 Opened cryosparc_P105_J67_007_volume_map_sharp.mrc as #4, grid size 300,300,300, pixel 2.12, shown at level 0.276, step 1, values float32 opened ChimeraX session > volume #4 level 0.2635 > volume #!4 style mesh > volume #!4 style surface > volume #!4 style image > volume #!4 style surface > volume #!4 style image > volume #!4 showOutlineBox true > volume #!4 style surface > select 152142 atoms, 155462 bonds, 8 pseudobonds, 19260 residues, 21 models selected > show #!2 target m > view #2 clip false > open /Users/z.kilic/Downloads/MmCPLs_fit-SCMC-PADI6_250529.cxs Opened cryosparc_P105_J56_006_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 2.12, shown at level 0.289, step 1, values float32 Opened cryosparc_P105_J67_007_volume_map_sharp.mrc as #4, grid size 300,300,300, pixel 2.12, shown at level 0.276, step 1, values float32 opened ChimeraX session > show #!2 target m > view #2 clip false > view #3 clip false > view #5 clip false > color #5 #cb002aff > color #6 #efef13ff > color #7 #71ef31ff > color #7 #efe919ff > color #8 #cb00efff > color #8 #24eaccff > open /Users/z.kilic/Downloads/MmCPLs_fit-SCMC-TUBB_250602.cxs Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.157, step 1, values float32 opened ChimeraX session > open /Users/z.kilic/Downloads/cryosparc_P105_J41_005_volume_map_sharp.mrc Opened cryosparc_P105_J41_005_volume_map_sharp.mrc as #6, grid size 400,400,400, pixel 2.12, shown at level 0.211, step 2, values float32 > hide #!2 models > hide #4 models > hide #5 models > hide #!6 models > close #6 > close #2 > close #1 > select add #3 22389 atoms, 22878 bonds, 16 pseudobonds, 2835 residues, 2 models selected > select add #4 25885 atoms, 26450 bonds, 16 pseudobonds, 3280 residues, 3 models selected > select add #5 29381 atoms, 30022 bonds, 16 pseudobonds, 3725 residues, 4 models selected > close #5 > close > open /Users/z.kilic/Downloads/cryosparc_P105_J41_005_volume_map_sharp.mrc Opened cryosparc_P105_J41_005_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 2.12, shown at level 0.211, step 2, values float32 > volume #1 level 0.2964 > open /Users/z.kilic/Downloads/8h93.cif 8h93.cif title: Structure of dimeric mouse SCMC core complex [more info...] Chain information for 8h93.cif #2 --- Chain | Description | UniProt A D | NACHT, LRR and PYD domains-containing protein 5 | NALP5_MOUSE 1-1059 B E | Transducin-like enhancer protein 6 | TLE6_MOUSE 1-581 C F | Oocyte-expressed protein homolog | OOEP_MOUSE 1-164 > ui mousemode right select > ui mousemode right ""translate selected models"" > hide #!1 models > show #!1 models > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > ui mousemode right ""move picked models"" > select ~sel & ##selected Nothing selected > select ~sel & ##selected Nothing selected > ui mousemode right ""move picked models"" > ui mousemode right ""translate selected models"" > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > view matrix models #2,1,0,0,55.847,0,1,0,53.724,0,0,1,169.99 > view matrix models #2,1,0,0,64.124,0,1,0,216.98,0,0,1,116.58 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.49935,-0.69873,0.51227,423.82,-0.15297,-0.51087,-0.84594,789,0.85279,-0.50079,0.14822,246 > view matrix models > #2,0.9364,-0.25098,0.24528,74.272,-0.037652,0.62305,0.78128,119.72,-0.3489,-0.74083,0.57397,459.89 > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > style sel stick Changed 22191 atom styles > style sel sphere Changed 22191 atom styles > style sel sphere Changed 22191 atom styles > style sel ball Changed 22191 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > nucleotides sel fill > style nucleic & sel stick Changed 0 atom styles > nucleotides sel atoms > style nucleic & sel stick Changed 0 atom styles > color sel bychain > show sel atoms > show sel cartoons > view matrix models > #2,-0.30691,-0.54497,0.78026,283.66,-0.30208,-0.72166,-0.62286,814.58,0.90253,-0.42686,0.056864,239.98 > view matrix models > #2,-0.69068,-0.4072,0.59762,381.84,-0.43316,-0.42881,-0.79278,819.78,0.57909,-0.80642,0.11979,379.88 > view matrix models > #2,0.49705,-0.80968,0.31202,278.35,-0.14893,-0.43385,-0.88859,781.47,0.85485,0.3952,-0.33623,163.77 > view matrix models > #2,0.69254,-0.66585,-0.27753,346.02,-0.65435,-0.41789,-0.63024,826.77,0.30367,0.61807,-0.7251,329.85 > view matrix models > #2,-0.50443,-0.85206,-0.13982,617.42,-0.79832,0.52192,-0.30046,571.02,0.32898,-0.03994,-0.94349,522.52 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.50443,-0.85206,-0.13982,640.44,-0.79832,0.52192,-0.30046,588.25,0.32898,-0.03994,-0.94349,581.95 > view matrix models > #2,-0.50443,-0.85206,-0.13982,886.17,-0.79832,0.52192,-0.30046,592.78,0.32898,-0.03994,-0.94349,641.62 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.8738,-0.43398,0.21939,788.25,-0.47546,0.85713,-0.19818,422.88,-0.10204,-0.27748,-0.9553,791.88 > view matrix models > #2,-0.8105,-0.57388,0.11728,829.92,-0.58507,0.7836,-0.20898,465.86,0.028025,-0.238,-0.97086,758.29 > view matrix models > #2,0.61848,-0.22214,0.75375,283.71,-0.78475,-0.22427,0.57782,542.42,0.04069,-0.94887,-0.31303,753.63 > view matrix models > #2,0.72274,-0.11565,0.68138,254.71,-0.6378,-0.49134,0.59312,565.4,0.26619,-0.86325,-0.42887,713.06 > view matrix models > #2,0.96581,-0.209,0.15342,349.45,-0.24962,-0.58965,0.76812,459.37,-0.070072,-0.78015,-0.62166,815.32 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.96581,-0.209,0.15342,343.9,-0.24962,-0.58965,0.76812,456.95,-0.070072,-0.78015,-0.62166,817.16 > view matrix models > #2,0.96581,-0.209,0.15342,319.55,-0.24962,-0.58965,0.76812,428.4,-0.070072,-0.78015,-0.62166,776.5 > fitmap #2 inMap #1 Fit molecule 8h93.cif (#2) to map cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) using 22191 atoms average map value = 0.258, steps = 208 shifted from previous position = 43.2 rotated from previous position = 36.1 degrees atoms outside contour = 10956, contour level = 0.29642 Position of 8h93.cif (#2) relative to cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.68400830 -0.72905873 -0.02461914 535.30062203 -0.43850573 -0.43791152 0.78482247 396.07759517 -0.58296265 -0.52602942 -0.61923152 808.30192434 Axis -0.90146663 0.38397019 0.19981192 Axis point 0.00000000 513.38405256 353.25900016 Rotation angle (degrees) 133.35899536 Shift along axis -168.96530276 > view matrix models > #2,0.68401,-0.72906,-0.024619,559.44,-0.43851,-0.43791,0.78482,392.35,-0.58296,-0.52603,-0.61923,810.21 > fitmap #2 inMap #1 Fit molecule 8h93.cif (#2) to map cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) using 22191 atoms average map value = 0.2754, steps = 216 shifted from previous position = 36.2 rotated from previous position = 33.4 degrees atoms outside contour = 10705, contour level = 0.29642 Position of 8h93.cif (#2) relative to cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.80502793 -0.38390859 -0.45226574 530.92464660 -0.07215614 -0.82007506 0.56768871 469.58963286 -0.58883241 -0.42437150 -0.68788466 799.74263778 Axis -0.94588219 0.13020982 0.29724113 Axis point 0.00000000 400.12703721 409.01986531 Rotation angle (degrees) 148.37146576 Shift along axis -203.33058251 > fitmap #2 inMap #1 Fit molecule 8h93.cif (#2) to map cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) using 22191 atoms average map value = 0.2754, steps = 44 shifted from previous position = 0.0162 rotated from previous position = 0.0738 degrees atoms outside contour = 10704, contour level = 0.29642 Position of 8h93.cif (#2) relative to cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.80544678 -0.38279999 -0.45245966 530.62922843 -0.07103662 -0.82027922 0.56753492 469.44251899 -0.58839559 -0.42497794 -0.68788404 799.78129105 Axis -0.94599853 0.12956527 0.29715251 Axis point 0.00000000 399.89281044 408.97622260 Rotation angle (degrees) 148.35970597 Shift along axis -203.49400987 > view matrix models > #2,0.80545,-0.3828,-0.45246,168.34,-0.071037,-0.82028,0.56753,389.07,-0.5884,-0.42498,-0.68788,889.57 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.78328,-0.43274,-0.44632,182.77,-0.11866,-0.80882,0.57596,394.99,-0.61023,-0.39818,-0.68489,887.73 > view matrix models > #2,0.21258,-0.92321,-0.32016,386.34,-0.65118,-0.37813,0.65801,397.2,-0.72854,0.068598,-0.68156,809.79 > view matrix models > #2,0.24834,-0.95911,0.13579,276.21,0.55437,0.25568,0.79202,-40.693,-0.79436,-0.12141,0.5952,557.67 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.24834,-0.95911,0.13579,434.01,0.55437,0.25568,0.79202,-13.444,-0.79436,-0.12141,0.5952,571.72 > view matrix models > #2,0.24834,-0.95911,0.13579,445.56,0.55437,0.25568,0.79202,27.465,-0.79436,-0.12141,0.5952,475.12 > view matrix models > #2,0.24834,-0.95911,0.13579,435.62,0.55437,0.25568,0.79202,99.979,-0.79436,-0.12141,0.5952,472.25 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.22596,-0.97287,0.04967,464.41,0.7873,0.21241,0.57883,109.79,-0.57368,-0.091688,0.81393,364.22 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.22596,-0.97287,0.04967,457.94,0.7873,0.21241,0.57883,92.976,-0.57368,-0.091688,0.81393,380.21 > fitmap #2 inMap #1 Fit molecule 8h93.cif (#2) to map cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) using 22191 atoms average map value = 0.328, steps = 92 shifted from previous position = 8.46 rotated from previous position = 21.1 degrees atoms outside contour = 6710, contour level = 0.29642 Position of 8h93.cif (#2) relative to cryosparc_P105_J41_005_volume_map_sharp.mrc (#1) coordinates: Matrix rotation and translation 0.55561031 -0.82553541 0.09893717 338.02722762 0.67842167 0.51892526 0.52005835 59.11245083 -0.48066756 -0.22182865 0.84838130 373.75183466 Axis -0.41812380 0.32666233 0.84762268 Axis point 265.58270833 365.15005250 0.00000000 Rotation angle (degrees) 62.51874388 Shift along axis 194.77311534 > hide target m > show target m > hide #!1 models > select /A/D 14957 atoms, 15221 bonds, 2 pseudobonds, 1898 residues, 2 models selected > select /C/F 1438 atoms, 1472 bonds, 178 residues, 1 model selected > select /B/E 5796 atoms, 5928 bonds, 2 pseudobonds, 734 residues, 2 models selected > show #!1 models > view matrix models > #2,0.55561,-0.82554,0.098937,345.44,0.67842,0.51893,0.52006,47.648,-0.48067,-0.22183,0.84838,423.89 > view matrix models > #2,0.55561,-0.82554,0.098937,528.38,0.67842,0.51893,0.52006,159.73,-0.48067,-0.22183,0.84838,295.74 > view matrix models > #2,0.55561,-0.82554,0.098937,581.92,0.67842,0.51893,0.52006,16.657,-0.48067,-0.22183,0.84838,302.89 > view matrix models > #2,0.55561,-0.82554,0.098937,562.98,0.67842,0.51893,0.52006,93.049,-0.48067,-0.22183,0.84838,371.66 > view matrix models > #2,0.55561,-0.82554,0.098937,631.89,0.67842,0.51893,0.52006,184.6,-0.48067,-0.22183,0.84838,358.78 > view matrix models > #2,0.55561,-0.82554,0.098937,557.81,0.67842,0.51893,0.52006,88.413,-0.48067,-0.22183,0.84838,373.51 > view matrix models > #2,0.55561,-0.82554,0.098937,546.89,0.67842,0.51893,0.52006,149.61,-0.48067,-0.22183,0.84838,405.68 > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > close > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > save /Users/z.kilic/Desktop/Chimeraimages/250408_25oocytesin20ul_figure.png > width 2000 height 1321 supersample 4 > view name front > view front > view list Named views: front > view front > save /Users/z.kilic/Desktop/Chimeraimages/listed.cxs includeMaps true > ui mousemode right clip > view name clipped > view list Named views: clipped, front > view clipped > clip off > select #19/A#19/B 6907 atoms, 7069 bonds, 870 residues, 1 model selected > select #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > select clear Drag select of 47 residues > select clear > select #2/E 2898 atoms, 2964 bonds, 1 pseudobond, 367 residues, 2 models selected > color sel red > color sel #6A5ACD > ui mousemode right clip > clip off > ui mousemode right clip > ui mousemode right translate > color #2/B #6A5acd > hide #!1 models > hide #!2 models > show #!1 models > hide #4-6,8-13,15,17-19,21-23#!2-3,7,14,16,20 target m > volume #1 color #b2b2b2 > color zone #1 near #2/B distance 5 > color zone #1 near #2-23 distance 5 > show #19 models > show #4 models > hide #!1 models > show #5 models > color #4,5,19 pink > show #!1 models > hide #4 models > hide #5 models > hide #19 models > color zone #1 near #2-23 distance 5 > hide #!1 models > show #18 models > hide #18 models > show #!1 models > hide #!1 models > show #!2 models > select #2/B 2898 atoms, 2964 bonds, 1 pseudobond, 367 residues, 2 models selected > save /Users/z.kilic/Desktop/Chimeraimages/TLE6_1.pdb models #2 selectedOnly > true > hide #!2 models > open /Users/z.kilic/Desktop/Chimeraimages/TLE6_1.pdb Summary of feedback from opening /Users/z.kilic/Desktop/Chimeraimages/TLE6_1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 97 PHE A 109 1 13 Start residue of secondary structure not found: HELIX 2 2 SER A 119 PHE A 129 1 11 Start residue of secondary structure not found: HELIX 3 3 GLY A 150 GLY A 165 1 16 Start residue of secondary structure not found: HELIX 4 4 ARG A 180 ILE A 182 1 3 Start residue of secondary structure not found: HELIX 5 5 SER A 189 CYS A 198 1 10 170 messages similar to the above omitted Chain information for TLE6_1.pdb #24 --- Chain | Description B | No description available > show #!1 models > volume #1 color #b2b2b245 > open /Users/z.kilic/Downloads/AF-P68373-F1-model_v4.pdb AF-P68373-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for tubulin α-1C chain (P68373) [more info...] Chain information for AF-P68373-F1-model_v4.pdb #25 --- Chain | Description | UniProt A | tubulin α-1C chain | TBA1C_MOUSE 1-449 Computing secondary structure > hide #!24 models > view > select add #25 6406 atoms, 6551 bonds, 1 pseudobond, 816 residues, 3 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,0.30996,0.86164,0.40188,293.94,-0.82022,0.4561,-0.34527,846.21,-0.4808,-0.2226,0.84811,420.6,#25,1,0,0,249.08,0,1,0,271.84,0,0,1,152.06 > view matrix models > #2,0.30996,0.86164,0.40188,235.05,-0.82022,0.4561,-0.34527,877.35,-0.4808,-0.2226,0.84811,413.2,#25,1,0,0,190.18,0,1,0,302.98,0,0,1,144.66 > view matrix models > #2,0.30996,0.86164,0.40188,244.63,-0.82022,0.4561,-0.34527,840.45,-0.4808,-0.2226,0.84811,517.06,#25,1,0,0,199.76,0,1,0,266.08,0,0,1,248.52 > view matrix models > #2,0.30996,0.86164,0.40188,291.78,-0.82022,0.4561,-0.34527,815.58,-0.4808,-0.2226,0.84811,511.63,#25,1,0,0,246.92,0,1,0,241.21,0,0,1,243.09 > view matrix models > #2,0.30996,0.86164,0.40188,284.02,-0.82022,0.4561,-0.34527,811.76,-0.4808,-0.2226,0.84811,511.92,#25,1,0,0,239.16,0,1,0,237.39,0,0,1,243.38 > view matrix models > #2,0.30996,0.86164,0.40188,291.93,-0.82022,0.4561,-0.34527,844.61,-0.4808,-0.2226,0.84811,502.51,#25,1,0,0,247.07,0,1,0,270.24,0,0,1,233.97 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.30996,0.86164,0.40188,525.84,-0.82022,0.4561,-0.34527,787.03,-0.4808,-0.2226,0.84811,525.98,#25,1,0,0,480.97,0,1,0,212.66,0,0,1,257.44 > view matrix models > #2,0.30996,0.86164,0.40188,664.42,-0.82022,0.4561,-0.34527,782.94,-0.4808,-0.2226,0.84811,535.22,#25,1,0,0,619.56,0,1,0,208.57,0,0,1,266.68 > select add #1 6406 atoms, 6551 bonds, 1 pseudobond, 816 residues, 5 models selected > view matrix models > #1,1,0,0,139.59,0,1,0,86.245,0,0,1,-18.369,#2,0.30996,0.86164,0.40188,804.01,-0.82022,0.4561,-0.34527,869.19,-0.4808,-0.2226,0.84811,516.85,#25,1,0,0,759.15,0,1,0,294.81,0,0,1,248.31 > view matrix models > #1,1,0,0,161.16,0,1,0,67.6,0,0,1,-22.536,#2,0.30996,0.86164,0.40188,825.58,-0.82022,0.4561,-0.34527,850.54,-0.4808,-0.2226,0.84811,512.68,#25,1,0,0,780.72,0,1,0,276.17,0,0,1,244.14 > undo > select subtract #1 6406 atoms, 6551 bonds, 1 pseudobond, 816 residues, 3 models selected > view matrix models > #2,0.30996,0.86164,0.40188,618.69,-0.82022,0.4561,-0.34527,805.42,-0.4808,-0.2226,0.84811,543.34,#25,1,0,0,573.83,0,1,0,231.05,0,0,1,274.8 > view matrix models > #2,0.30996,0.86164,0.40188,701.37,-0.82022,0.4561,-0.34527,834.84,-0.4808,-0.2226,0.84811,531.56,#25,1,0,0,656.51,0,1,0,260.47,0,0,1,263.02 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.51402,0.058056,-0.85581,336.76,0.8573,-0.001396,0.51482,-229.81,0.028694,-0.99831,-0.050489,8.0598,#25,-0.13458,-0.099646,-0.98588,664.78,0.47142,-0.88156,0.024751,248.74,-0.87158,-0.46143,0.16561,267.72 > view matrix models > #2,0.20766,-0.044497,-0.97719,488.78,0.93369,0.30692,0.18444,-216.43,0.29171,-0.95069,0.10528,-129.79,#25,-0.36668,0.14677,-0.9187,667.64,0.62799,-0.68953,-0.36081,248.33,-0.68642,-0.70923,0.16067,265.23 > view matrix models > #2,-0.017287,-0.34616,-0.93801,552.46,0.99855,-0.053788,0.0014471,-347.88,-0.050955,-0.93663,0.34659,86.845,#25,-0.68059,0.18016,-0.71017,670.22,0.26375,-0.84406,-0.4669,250.48,-0.68354,-0.50507,0.52694,266.1 > view matrix models > #2,-0.70412,-0.68962,-0.16925,911.15,-0.025588,0.26284,-0.9645,291.99,0.70962,-0.67479,-0.20271,-325.37,#25,-0.88047,0.32143,0.34851,672.44,-0.16907,0.47388,-0.8642,259.46,-0.44293,-0.81983,-0.3629,262.84 > view matrix models > #2,-0.47577,-0.84196,0.25446,758.12,-0.64827,0.14013,-0.74841,641.08,0.59447,-0.52103,-0.61249,-238.45,#25,-0.77067,-0.081642,0.63198,669.88,-0.38096,0.85404,-0.35424,262.76,-0.51082,-0.51376,-0.68929,264.66 > view matrix models > #2,-0.46476,-0.84565,0.26244,751.07,-0.66285,0.13578,-0.73634,649.21,0.58705,-0.51618,-0.62364,-233.39,#25,-0.76723,-0.095108,0.63428,669.79,-0.38438,0.85985,-0.33602,262.81,-0.51342,-0.50161,-0.69626,264.73 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.46476,-0.84565,0.26244,677.11,-0.66285,0.13578,-0.73634,704.3,0.58705,-0.51618,-0.62364,-172.6,#25,-0.76723,-0.095108,0.63428,595.83,-0.38438,0.85985,-0.33602,317.9,-0.51342,-0.50161,-0.69626,325.52 > view matrix models > #2,-0.46476,-0.84565,0.26244,589.33,-0.66285,0.13578,-0.73634,778.85,0.58705,-0.51618,-0.62364,-102.78,#25,-0.76723,-0.095108,0.63428,508.05,-0.38438,0.85985,-0.33602,392.46,-0.51342,-0.50161,-0.69626,395.34 > view matrix models > #2,-0.46476,-0.84565,0.26244,564.97,-0.66285,0.13578,-0.73634,692.47,0.58705,-0.51618,-0.62364,-56.063,#25,-0.76723,-0.095108,0.63428,483.69,-0.38438,0.85985,-0.33602,306.08,-0.51342,-0.50161,-0.69626,442.06 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.10979,0.87899,0.46403,640.59,-0.90347,0.28287,-0.32208,887.5,-0.41436,-0.38388,0.82519,630.48,#25,0.97788,0.15064,0.1451,471.23,-0.16574,0.98126,0.098258,304.94,-0.12758,-0.12013,0.98453,440.82 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.10979,0.87899,0.46403,663.59,-0.90347,0.28287,-0.32208,808.72,-0.41436,-0.38388,0.82519,510.95,#25,0.97788,0.15064,0.1451,494.23,-0.16574,0.98126,0.098258,226.16,-0.12758,-0.12013,0.98453,321.29 > view matrix models > #2,0.10979,0.87899,0.46403,655.1,-0.90347,0.28287,-0.32208,822.23,-0.41436,-0.38388,0.82519,546.15,#25,0.97788,0.15064,0.1451,485.74,-0.16574,0.98126,0.098258,239.67,-0.12758,-0.12013,0.98453,356.49 > view matrix models > #2,0.10979,0.87899,0.46403,571.83,-0.90347,0.28287,-0.32208,902.85,-0.41436,-0.38388,0.82519,559.55,#25,0.97788,0.15064,0.1451,402.47,-0.16574,0.98126,0.098258,320.29,-0.12758,-0.12013,0.98453,369.89 > view matrix models > #2,0.10979,0.87899,0.46403,594.64,-0.90347,0.28287,-0.32208,874.18,-0.41436,-0.38388,0.82519,515.58,#25,0.97788,0.15064,0.1451,425.28,-0.16574,0.98126,0.098258,291.62,-0.12758,-0.12013,0.98453,325.92 > view matrix models > #2,0.10979,0.87899,0.46403,593.25,-0.90347,0.28287,-0.32208,831.22,-0.41436,-0.38388,0.82519,498.53,#25,0.97788,0.15064,0.1451,423.89,-0.16574,0.98126,0.098258,248.66,-0.12758,-0.12013,0.98453,308.87 > view matrix models > #2,0.10979,0.87899,0.46403,591.35,-0.90347,0.28287,-0.32208,828.12,-0.41436,-0.38388,0.82519,504.78,#25,0.97788,0.15064,0.1451,421.99,-0.16574,0.98126,0.098258,245.56,-0.12758,-0.12013,0.98453,315.11 > view matrix models > #2,0.10979,0.87899,0.46403,604.3,-0.90347,0.28287,-0.32208,842.1,-0.41436,-0.38388,0.82519,470.05,#25,0.97788,0.15064,0.1451,434.95,-0.16574,0.98126,0.098258,259.54,-0.12758,-0.12013,0.98453,280.39 > view matrix models > #2,0.10979,0.87899,0.46403,609.57,-0.90347,0.28287,-0.32208,811.45,-0.41436,-0.38388,0.82519,439.58,#25,0.97788,0.15064,0.1451,440.22,-0.16574,0.98126,0.098258,228.89,-0.12758,-0.12013,0.98453,249.92 > view matrix models > #2,0.10979,0.87899,0.46403,584.62,-0.90347,0.28287,-0.32208,775.21,-0.41436,-0.38388,0.82519,437.88,#25,0.97788,0.15064,0.1451,415.26,-0.16574,0.98126,0.098258,192.65,-0.12758,-0.12013,0.98453,248.22 > view matrix models > #2,0.10979,0.87899,0.46403,581.21,-0.90347,0.28287,-0.32208,843.42,-0.41436,-0.38388,0.82519,487.18,#25,0.97788,0.15064,0.1451,411.85,-0.16574,0.98126,0.098258,260.86,-0.12758,-0.12013,0.98453,297.51 > view matrix models > #2,0.10979,0.87899,0.46403,410.34,-0.90347,0.28287,-0.32208,832.98,-0.41436,-0.38388,0.82519,437.6,#25,0.97788,0.15064,0.1451,240.98,-0.16574,0.98126,0.098258,250.42,-0.12758,-0.12013,0.98453,247.94 > view matrix models > #2,0.10979,0.87899,0.46403,440.64,-0.90347,0.28287,-0.32208,851.92,-0.41436,-0.38388,0.82519,466.32,#25,0.97788,0.15064,0.1451,271.28,-0.16574,0.98126,0.098258,269.36,-0.12758,-0.12013,0.98453,276.66 > view matrix models > #2,0.10979,0.87899,0.46403,467.2,-0.90347,0.28287,-0.32208,839.95,-0.41436,-0.38388,0.82519,439.9,#25,0.97788,0.15064,0.1451,297.84,-0.16574,0.98126,0.098258,257.39,-0.12758,-0.12013,0.98453,250.24 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.13076,-0.51217,-0.84887,69.916,0.65456,0.68768,-0.31408,13.122,0.74462,-0.51457,0.42517,-294.55,#25,-0.74191,-0.04776,-0.66879,310.23,0.6692,-0.11478,-0.73416,246.18,-0.041704,-0.99224,0.11712,245.78 > view matrix models > #2,-0.34175,-0.43583,-0.83262,368.49,0.70126,0.47156,-0.53467,-75.038,0.62566,-0.7666,0.14448,-295.66,#25,-0.81607,0.369,-0.44482,312.61,0.40881,-0.1755,-0.89559,247.92,-0.40854,-0.91271,-0.007635,248.95 > view matrix models > #2,-0.64733,-0.17205,-0.74253,615.63,0.4655,0.68216,-0.56388,113.07,0.60355,-0.71067,-0.3615,-291.08,#25,-0.6473,0.70886,-0.28021,312.77,0.50546,0.12402,-0.85389,248.47,-0.57054,-0.69436,-0.43857,251.11 > view matrix models > #2,-0.77526,-0.40639,-0.48355,647.18,0.3776,0.3155,-0.87056,65.38,0.50635,-0.8575,-0.091143,-256.58,#25,-0.78479,0.61749,0.053107,313.46,0.039034,0.13476,-0.99011,252.11,-0.61853,-0.77495,-0.12986,251.15 > view matrix models > #2,0.5457,-0.82012,0.17211,-204.73,0.098882,-0.14093,-0.98507,117.76,0.83213,0.55457,0.0041896,-111.99,#25,-0.46833,-0.88107,0.066158,304.58,-0.48666,0.19473,-0.85161,256.44,0.73745,-0.43103,-0.51998,242.13 > view matrix models > #2,-0.18095,-0.97416,0.13517,187.68,-0.63394,0.010451,-0.77331,596.62,0.75192,-0.22562,-0.61945,-275.49,#25,-0.84114,-0.34257,0.41849,309.8,-0.49827,0.79174,-0.35339,259.12,-0.21027,-0.50576,-0.83665,249.11 > view matrix models > #2,-0.90742,0.01432,0.41998,863.59,0.24374,0.83207,0.49825,325.41,-0.34232,0.55448,-0.75853,550.83,#25,-0.10015,0.60581,0.78928,308.17,0.99273,0.0075602,0.12016,244.26,0.066825,0.79558,-0.60216,252.58 > view matrix models > #2,-0.62412,0.11801,0.77236,735.42,0.7208,0.46846,0.51088,-42.459,-0.30153,0.87557,-0.37744,618.85,#25,0.21862,0.29907,0.92885,304.4,0.83237,-0.55394,-0.017559,243.08,0.50927,0.77699,-0.37004,249.09 > view matrix models > #2,-0.83752,-0.52252,-0.15981,670.53,-0.51392,0.85262,-0.094459,753.55,0.18561,0.0030187,-0.98262,98.308,#25,-0.77404,0.5038,0.38345,312.91,0.5374,0.84302,-0.022819,251.36,-0.33476,0.1884,-0.92328,253.05 > view matrix models > #2,-0.27666,-0.9591,-0.059858,239.55,-0.56135,0.21186,-0.8,600.04,0.77996,-0.18773,-0.597,-282.19,#25,-0.93621,-0.18986,0.29575,311.18,-0.31296,0.83328,-0.45575,257.86,-0.15992,-0.51924,-0.83954,248.66 > view matrix models > #2,-0.51077,-0.36329,0.77919,554.92,-0.79076,-0.15712,-0.59161,657.74,0.33736,-0.91833,-0.20703,-175.83,#25,-0.15821,-0.015791,0.98728,305.96,-0.61824,0.7812,-0.086577,260.02,-0.7699,-0.62408,-0.13336,252.97 > view matrix models > #2,-0.034899,-0.23678,0.97094,311.18,-0.25442,-0.93742,-0.23775,171.01,0.96646,-0.25532,-0.027525,-384.16,#25,0.17536,-0.41461,0.89294,301.66,-0.98212,-0.13679,0.12936,258.9,0.068509,-0.89966,-0.43118,245.29 > view matrix models > #2,-0.74394,0.66751,-0.031528,901.62,-0.66405,-0.74372,-0.076964,466.26,-0.074822,-0.036321,0.99654,328.23,#25,0.33189,0.92553,0.18235,306.17,-0.87757,0.23203,0.41955,259.7,0.346,-0.29927,0.88923,245.81 > view matrix models > #2,-0.3241,-0.41757,-0.84888,361.65,0.63344,0.57068,-0.52257,-10.949,0.70265,-0.70708,0.079552,-329.99,#25,-0.8014,0.36847,-0.47116,312.49,0.47805,-0.078843,-0.87479,247.81,-0.35948,-0.92629,-0.11296,248.5 > view matrix models > #2,-0.82754,-0.2037,-0.52316,724.31,0.499,0.16015,-0.85168,-42.393,0.25727,-0.96585,-0.030883,-132.06,#25,-0.64226,0.76648,-0.0004723,313,-0.049608,-0.042183,-0.99788,252.03,-0.76488,-0.64088,0.065116,252.87 > view matrix models > #2,0.096334,-0.62715,-0.77292,66.416,0.31349,0.75613,-0.57445,220.11,0.94469,-0.18696,0.26944,-342.38,#25,-0.82113,-0.098189,-0.56223,310.63,0.51782,0.28608,-0.80624,249.07,0.24001,-0.95316,-0.18407,243.75 > view matrix models > #2,-0.80024,-0.59498,-0.074936,634.98,0.13727,-0.060107,-0.98871,113.95,0.58376,-0.80149,0.12978,-279.72,#25,-0.79082,0.41087,0.45364,312.65,-0.40658,0.20136,-0.89115,255.84,-0.45749,-0.88918,0.0078092,249.43 > view matrix models > #2,0.18339,-0.74059,-0.64645,-6.5005,-0.69731,-0.56153,0.44548,551.41,-0.69292,0.36908,-0.61939,720.67,#25,-0.84107,-0.265,-0.47158,310.07,-0.52094,0.16202,0.83807,256.67,-0.14568,0.95054,-0.27432,254.9 > view matrix models > #2,-0.77889,0.041247,0.6258,802.66,0.41694,0.77945,0.46757,209.08,-0.46849,0.62511,-0.62431,647.99,#25,0.045606,0.4416,0.89605,306.34,0.98874,-0.14791,0.022573,243.62,0.14251,0.88493,-0.44338,252.38 > view matrix models > #2,-0.64198,-0.72257,0.25643,525.35,-0.67471,0.69126,0.25869,825.84,-0.36418,-0.0069437,-0.9313,423.78,#25,-0.71853,0.10846,0.68699,310.8,0.49044,0.77938,0.38992,251.48,-0.49313,0.61709,-0.6132,256.13 > view matrix models > #2,0.21443,-0.97334,0.081469,-48.597,-0.82246,-0.22492,-0.52246,663.47,0.52685,0.045026,-0.84876,-88.129,#25,-0.73946,-0.64795,0.18267,307.69,-0.6587,0.7524,0.0024061,260.21,-0.139,-0.11854,-0.98317,250.22 > view matrix models > #2,0.49752,-0.29449,0.81594,-24.431,0.4095,-0.74947,-0.5202,-189.95,0.76471,0.59293,-0.25228,-74.02,#25,0.22837,-0.82411,0.51835,299.47,-0.7279,-0.4981,-0.47123,255.35,0.64654,-0.26969,-0.71362,243.51 > view matrix models > #2,-0.72411,0.024751,0.68924,769.04,0.6778,0.21025,0.70454,-69.652,-0.12747,0.97733,-0.16902,548.74,#25,0.073867,0.36724,0.92719,305.81,0.67439,-0.70331,0.22484,243.67,0.73467,0.60868,-0.29962,246.63 > view matrix models > #2,-0.66528,-0.69084,-0.2831,523.48,0.72454,-0.68889,-0.021574,-340.83,-0.18012,-0.21947,0.95885,345.73,#25,-0.91524,0.32833,0.23354,313.24,-0.37766,-0.90104,-0.2133,250.93,0.1404,-0.28342,0.94866,247.47 > view matrix models > #2,-0.11118,-0.68342,-0.72151,178.24,0.94824,0.14436,-0.28285,-287.77,0.29746,-0.71561,0.63199,-68.313,#25,-0.91328,0.0286,-0.40633,311.9,0.30463,-0.61426,-0.72793,246.85,-0.27041,-0.78858,0.55228,248.45 > view matrix models > #2,-0.17814,-0.36786,-0.91266,284.21,0.77395,0.52039,-0.36082,-99.1,0.60767,-0.77063,0.192,-283.92,#25,-0.73895,0.29345,-0.6065,311.68,0.54328,-0.27288,-0.79397,246.47,-0.39849,-0.9162,0.042219,248.86 > view matrix models > #2,0.17017,-0.065608,-0.98323,146.25,0.97304,0.1688,0.15715,-277.8,0.15566,-0.98346,0.092565,-70.738,#25,-0.39892,0.16998,-0.90109,308.5,0.51021,-0.77537,-0.37213,244.6,-0.76194,-0.6082,0.22259,253 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.17017,-0.065608,-0.98323,135.62,0.97304,0.1688,0.15715,-268.7,0.15566,-0.98346,0.092565,-58.823,#25,-0.39892,0.16998,-0.90109,297.86,0.51021,-0.77537,-0.37213,253.69,-0.76194,-0.6082,0.22259,264.92 > fitmap sel inMap #1 Fit molecules 8h93 (#2), AF-P68373-F1-model_v4.pdb (#25) to map cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) using 6406 atoms average map value = 0.1611, steps = 2000 shifted from previous position = 86.5 rotated from previous position = 16.4 degrees atoms outside contour = 4181, contour level = 0.030497 Position of 8h93 (#2) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation 0.40846653 -0.15213835 -0.90000500 -7.88554045 0.88830939 0.29300806 0.35362791 -172.89592701 0.20990836 -0.94392806 0.25482991 -81.83308368 Axis -0.64893288 -0.55508918 0.52034808 Axis point 0.00000000 -167.71501032 61.77544700 Rotation angle (degrees) 91.25188343 Shift along axis 58.50815679 Position of AF-P68373-F1-model_v4.pdb (#25) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation -0.36616872 -0.09367547 -0.92582146 310.96641409 0.66992383 -0.71706479 -0.19240618 260.58047602 -0.64585023 -0.69068299 0.32532212 256.48745701 Axis -0.52240849 -0.29353031 0.80058062 Axis point 199.42371038 223.82166339 0.00000000 Rotation angle (degrees) 151.51664490 Shift along axis -33.60087451 > fitmap sel inMap #1 Fit molecules 8h93 (#2), AF-P68373-F1-model_v4.pdb (#25) to map cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) using 6406 atoms average map value = 0.161, steps = 2000 shifted from previous position = 4.75 rotated from previous position = 0.884 degrees atoms outside contour = 4158, contour level = 0.030497 Position of 8h93 (#2) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation 0.40543119 -0.16672816 -0.89879211 -9.70080360 0.89174892 0.28835328 0.34876387 -176.48863996 0.20102089 -0.94289665 0.26558707 -76.18343902 Axis -0.64596356 -0.55002000 0.52934778 Axis point 0.00000000 -167.19580125 65.50828346 Rotation angle (degrees) 91.16399964 Shift along axis 63.01111372 Position of AF-P68373-F1-model_v4.pdb (#25) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation -0.37919325 -0.09825903 -0.92008567 310.82783453 0.66502448 -0.72032960 -0.19714893 260.35638798 -0.64339327 -0.68663704 0.33848879 256.16722344 Axis -0.51632187 -0.29186068 0.80512674 Axis point 198.17832949 222.82212096 0.00000000 Rotation angle (degrees) 151.70479577 Shift along axis -30.22791745 > view matrix models > #2,0.40543,-0.16673,-0.89879,-16.254,0.89175,0.28835,0.34876,-184.97,0.20102,-0.9429,0.26559,-63.697,#25,-0.37919,-0.098259,-0.92009,304.27,0.66502,-0.72033,-0.19715,251.88,-0.64339,-0.68664,0.33849,268.65 > ui mousemode right ""rotate selected models"" > view matrix models > #2,-0.50351,-0.45346,-0.73542,461.39,-0.65122,0.75858,-0.02188,824,0.56779,0.4679,-0.67726,11.739,#25,-0.84234,0.46009,-0.28069,310.29,0.44297,0.88768,0.12568,260.52,0.30699,-0.018467,-0.95153,264.1 > view matrix models > #2,-0.88085,-0.46948,-0.060731,710.06,-0.29423,0.44246,0.84714,575.24,-0.37085,0.76408,-0.52788,644.01,#25,-0.70196,0.52933,0.47651,309.55,0.63049,0.15065,0.76144,255.95,0.33127,0.83493,-0.43949,267.61 > view matrix models > #2,-0.31046,-0.8841,-0.34925,261.94,-0.93827,0.22604,0.26185,880.44,-0.15256,0.40898,-0.8997,414.92,#25,-0.99836,-0.028012,0.04987,309.42,0.0091643,0.78227,0.62287,263.45,-0.05646,0.62231,-0.78073,269.67 > view matrix models > #2,-0.72039,-0.69133,-0.055599,562.85,-0.68234,0.72082,-0.12181,829.23,0.12428,-0.04981,-0.991,138.7,#25,-0.84132,0.29476,0.4531,309.62,0.36063,0.93049,0.064306,261.34,-0.40265,0.2175,-0.88914,270.6 > view matrix models > #2,-0.25223,-0.88067,-0.40099,226.04,-0.94513,0.1353,0.29736,864.6,-0.20763,0.45399,-0.86648,459.59,#25,-0.99815,-0.056337,-0.02277,309.29,-0.056874,0.73425,0.67649,263.76,-0.021393,0.67654,-0.7361,269.64 > view matrix models > #2,-0.6495,-0.75418,-0.096775,504.26,-0.75484,0.65485,-0.037284,860.22,0.091492,0.048833,-0.99461,181.26,#25,-0.89004,0.22216,0.39808,309.68,0.31529,0.93068,0.18553,261.7,-0.32927,0.29064,-0.89839,270.35 > view matrix models > #2,-0.92196,-0.22146,0.31772,809.21,0.083533,0.68736,0.7215,403.93,-0.37817,0.69173,-0.61522,627.52,#25,-0.34891,0.5455,0.76204,306.91,0.9081,-0.0041246,0.41874,253.11,0.23156,0.8381,-0.49393,268.39 > view matrix models > #2,-0.86655,-0.15469,0.47452,798.89,0.1575,0.81742,0.5541,383.65,-0.47359,0.55489,-0.68397,648.77,#25,-0.21118,0.47637,0.85351,305.56,0.97581,0.052323,0.21224,252.82,0.056447,0.87769,-0.4759,269.91 > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.86655,-0.15469,0.47452,807.36,0.1575,0.81742,0.5541,387.58,-0.47359,0.55489,-0.68397,640.2,#25,-0.21118,0.47637,0.85351,314.02,0.97581,0.052323,0.21224,256.75,0.056447,0.87769,-0.4759,261.34 > fitmap sel inMap #1 Fit molecules 8h93 (#2), AF-P68373-F1-model_v4.pdb (#25) to map cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) using 6406 atoms average map value = 0.1783, steps = 2000 shifted from previous position = 102 rotated from previous position = 19.4 degrees atoms outside contour = 3704, contour level = 0.030497 Position of 8h93 (#2) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation -0.83161999 0.16063853 0.53160459 859.26924671 0.45017723 0.75553071 0.47593465 194.12473878 -0.32519015 0.63511306 -0.70063026 573.53852436 Axis 0.17334105 0.93302670 0.31529995 Axis point 465.34415069 0.00000000 153.54559079 Rotation angle (degrees) 152.66785487 Shift along axis 510.90686897 Position of AF-P68373-F1-model_v4.pdb (#25) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation 0.09427994 0.57182934 0.81493711 307.75367869 0.98179821 -0.18897269 0.01901527 253.51362926 0.16487435 0.79831104 -0.57923737 263.16344934 Axis 0.71200252 0.59392895 0.37456750 Axis point 0.00000000 -19.96379430 45.48400959 Rotation angle (degrees) 146.82101143 Shift along axis 468.26295414 > ui mousemode right translate > volume #1 color #bebebe45 > volume #1 level 0.2432 > fitmap sel inMap #1 Fit molecules 8h93 (#2), AF-P68373-F1-model_v4.pdb (#25) to map cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) using 6406 atoms average map value = 0.1832, steps = 2000 shifted from previous position = 64.1 rotated from previous position = 11.6 degrees atoms outside contour = 5384, contour level = 0.24321 Position of 8h93 (#2) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation -0.86254530 0.28244181 0.41981213 901.21029980 0.44747259 0.81310106 0.37233713 204.62051088 -0.23618611 0.50901206 -0.82772147 484.28638066 Axis 0.19804865 0.95057347 0.23913765 Axis point 463.68618889 0.00000000 141.09333441 Rotation angle (degrees) 159.81491141 Shift along axis 488.80141754 Position of AF-P68373-F1-model_v4.pdb (#25) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation 0.14471788 0.69134830 0.70788011 307.53283227 0.98893135 -0.12472704 -0.08036138 253.47516432 0.03273408 0.71167457 -0.70174624 262.49946341 Axis 0.73170649 0.62372009 0.27491611 Axis point 0.00000000 -31.92650409 67.34996258 Rotation angle (degrees) 147.23291894 Shift along axis 455.28665213 > volume #1 level 0.1 > fitmap sel inMap #1 Fit molecules 8h93 (#2), AF-P68373-F1-model_v4.pdb (#25) to map cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) using 6406 atoms average map value = 0.1939, steps = 2000 shifted from previous position = 62.5 rotated from previous position = 11.2 degrees atoms outside contour = 4346, contour level = 0.1 Position of 8h93 (#2) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation -0.75287749 0.38597360 0.53310398 866.79949185 0.60378811 0.72741751 0.32604244 88.84173006 -0.26194540 0.56735186 -0.78070254 516.33038684 Axis 0.28093882 0.92561753 0.25358542 Axis point 468.74206336 0.00000000 155.97041585 Rotation angle (degrees) 154.56608885 Shift along axis 456.68494399 Position of AF-P68373-F1-model_v4.pdb (#25) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation 0.31344690 0.60950109 0.72818916 307.10943627 0.94495045 -0.27603603 -0.17570644 252.18102258 0.09391318 0.74317731 -0.66247097 263.15758719 Axis 0.78817407 0.54405128 0.28773224 Axis point 0.00000000 -6.88429254 76.47089390 Rotation angle (degrees) 144.34386631 Shift along axis 454.97402417 > save /Users/z.kilic/Desktop/Chimeraimages/tuba1c_1.pdb models #25 > hide #25 models > open /Users/z.kilic/Desktop/Chimeraimages/tuba1c_1.pdb tuba1c_1.pdb title: Alphafold monomer V2.0 prediction for tubulin α-1C chain (P68373) [more info...] Chain information for tuba1c_1.pdb #26 --- Chain | Description | UniProt A | tubulin α-1C chain | TBA1C_MOUSE 1-449 > view orient > turn z 10 > turn y 180 > volume #1 color #bebebe > lighting soft > turn y 180 > turn x 180 > turn x 90 > turn x -90 > clip front Missing ""front"" keyword's argument > clip front 10 > clip front -10 > turn x 90 > turn x -90 > clip off > select #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > volume zone #1 nearAtoms sel > volume zone #1 nearAtoms sel range 4 newMap true Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc zone as #27, grid size 300,300,300, pixel 2.12, shown at step 1, values float32 > select add #27 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 4 models selected > view sel No displayed objects specified. > clip off > hide #26 models > show #!1 models > volume unzone #1 > volume zone #2 range 4 newMap true Missing required ""near_atoms"" argument > volume zone #2 nearAtoms sel range 4 newMap true > volume zone #1 nearAtoms sel range 4 newMap true Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc zone as #28, grid size 300,300,300, pixel 2.12, shown at step 1, values float32 > hide #!27 models > select subtract #27 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > view sel No displayed objects specified. > select add #28 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 4 models selected > view sel No displayed objects specified. > select subtract #2 2 models selected > show #!2 models > show #!1 models > volume #1 color #bebebe > lighting simple > volume #1 color #bebebebc > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 4 models selected > ui mousemode right ""translate selected models"" > view matrix models > #2,-0.75288,0.38597,0.5331,289.77,0.60379,0.72742,0.32604,-81.732,-0.26195,0.56735,-0.7807,492.83,#28,1,0,0,-577.03,0,1,0,-170.57,0,0,1,-23.501 > view matrix models > #2,-0.75288,0.38597,0.5331,244.24,0.60379,0.72742,0.32604,-76.908,-0.26195,0.56735,-0.7807,489.85,#28,1,0,0,-622.56,0,1,0,-165.75,0,0,1,-26.482 > view matrix models > #2,-0.75288,0.38597,0.5331,231.94,0.60379,0.72742,0.32604,-85.471,-0.26195,0.56735,-0.7807,489.65,#28,1,0,0,-634.86,0,1,0,-174.31,0,0,1,-26.679 > view matrix models > #2,-0.75288,0.38597,0.5331,243.72,0.60379,0.72742,0.32604,-107.74,-0.26195,0.56735,-0.7807,479.89,#28,1,0,0,-623.08,0,1,0,-196.58,0,0,1,-36.436 > ui mousemode right ""rotate selected models"" > view matrix models > #2,0.33668,0.30294,0.89156,-62.524,0.91877,-0.31302,-0.2406,190.99,0.20619,0.90014,-0.38372,207.93,#28,0.33874,0.71433,-0.61236,-103.43,-0.9408,0.2486,-0.23043,1103.4,-0.012368,0.65416,0.75625,-229.94 > view matrix models > #2,0.79161,0.46782,0.39306,-77.705,0.58627,-0.40025,-0.70433,395.12,-0.17218,0.788,-0.59111,365.56,#28,-0.20587,0.94642,-0.2488,145.13,-0.97136,-0.16681,0.16922,1164.5,0.11865,0.27652,0.95366,-254.26 > view matrix models > #2,0.9435,0.27508,0.18476,-17.78,0.29577,-0.44765,-0.84388,502.81,-0.14943,0.85085,-0.50371,325.53,#28,-0.50567,0.83002,-0.23532,468.29,-0.84533,-0.42218,0.32737,1104,0.17237,0.36447,0.91512,-328.77 > view matrix models > #2,0.69332,-0.71248,0.10809,274.04,-0.50872,-0.59014,-0.62685,657.47,0.5104,0.37961,-0.77161,350.64,#28,-0.73936,-0.064409,-0.67023,1266.7,-0.17895,-0.94082,0.28782,747.56,-0.6491,0.33274,0.68407,530.51 > view matrix models > #2,0.67142,-0.47311,0.57041,113.94,-0.28667,-0.87559,-0.3888,614.58,0.68339,0.097527,-0.72351,363.69,#28,-0.38402,0.24723,-0.88961,884.17,-0.3294,-0.93677,-0.11814,1044.3,-0.86257,0.24767,0.44117,861.57 > ui mousemode right ""translate selected models"" > view matrix models > #2,0.67142,-0.47311,0.57041,59.389,-0.28667,-0.87559,-0.3888,562.64,0.68339,0.097527,-0.72351,342.29,#28,-0.38402,0.24723,-0.88961,829.62,-0.3294,-0.93677,-0.11814,992.39,-0.86257,0.24767,0.44117,840.18 > fitmap sel inMap #1 Fit molecule 8h93 (#2) to map cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) using 22191 atoms average map value = 0.1569, steps = 124 shifted from previous position = 21.5 rotated from previous position = 16.2 degrees atoms outside contour = 12158, contour level = 0.1 Position of 8h93 (#2) relative to cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc (#1) coordinates: Matrix rotation and translation 0.84971444 -0.31089803 0.42582598 15.37291968 -0.18259588 -0.93118987 -0.31550621 545.81479199 0.49461510 0.19033611 -0.84801419 375.38692904 Axis 0.96099369 -0.13068481 0.24374702 Axis point 0.00000000 248.38331779 224.10325047 Rotation angle (degrees) 164.74074120 Shift along axis 34.94302001 > ui mousemode right ""translate selected models"" > ui mousemode right translate > select clear > volume zone #1 nearAtoms #2 range 4 newMap true Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc zone as #29, grid size 300,300,300, pixel 2.12, shown at step 1, values float32 > color #29 #b2b2ff75 models > color #29 #e5e9fa75 models > color #29 #e5e9fa2f models > color #29 #e1e5f62f models > color #29 #e1e5f62e models > color #29 white > transparency #29 0 > color zone #29 near #2 distance 4 > transparency #29 60 > transparency #29 0 > color zone #29 near #2 distance 4 > transparency #29 60 > transparency #29 \0 ; color zone #29 near #2 distance 4 Missing or invalid ""percent"" argument: Expected a number > transparency #29 0 > color zone #29 near #2 distance 4 > transparency #29 60 > color zone #29 near #2 distance 4 > transparency #29 60 > color zone #29 near #2 distance 4 > hide #!29 models > hide #!28 models > show #!1 models > show #!3 models > show #4 models > show #5 models > show #6 models > show #4-6,8-13,15,17-19,21-23,25-26#!2-3,7,14,16,20,24 target m > color #29 #e1e5f61f models > color #29 #e1e5f6ff models > color #29 #e1e5f616 models > select add #1 2 models selected > select subtract #1 Nothing selected > color #1 #bebebe54 models > hide #4-6,8-13,15,17-19,21-23,25-26#!2-3,7,14,16,20,24 target m > color #1 #00000054 models > color #1 #bebebe54 models > color #1 #bebebeff models > lighting soft > transparency #29 60 > color zone #29 near #2 distance 4 > view front > lighting full > lighting soft > lighting simple > lighting soft > lighting shadows true intensity 0.5 > graphics silhouettes false > lighting shadows false > lighting flat > lighting full > lighting soft > set bgColor white > set bgColor gray > set bgColor #80808000 > set bgColor black > set bgColor transparent > set bgColor white > set bgColor #ffffff00 > close #1 > close #7 > close #16 > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > select add #1 2 models selected > select subtract #1 Nothing selected > select add #1 2 models selected > select subtract #1 Nothing selected > select add #1 2 models selected > select subtract #1 Nothing selected > color #2 #EF767A > help help:devel > close session > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs format session Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > ui tool show Log > ui tool show ""File History"" > open /Users/z.kilic/Downloads/AF-P68373-F1-model_v4.pdb AF-P68373-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for tubulin α-1C chain (P68373) [more info...] Chain information for AF-P68373-F1-model_v4.pdb #24 --- Chain | Description | UniProt A | tubulin α-1C chain | TBA1C_MOUSE 1-449 Computing secondary structure > open /Users/z.kilic/Downloads/AF-P68373-F1-model_v4.pdb AF-P68373-F1-model_v4.pdb title: Alphafold monomer V2.0 prediction for tubulin α-1C chain (P68373) [more info...] Chain information for AF-P68373-F1-model_v4.pdb #25 --- Chain | Description | UniProt A | tubulin α-1C chain | TBA1C_MOUSE 1-449 Computing secondary structure > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs format session Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > open /Users/z.kilic/Downloads/MmCPLs_fit-SCMC-TUBB_250602.cxs format session Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.157, step 1, values float32 opened ChimeraX session > open /Users/z.kilic/Downloads/cryosparc_P105_J41_005_volume_map_sharp.mrc > format mrc Opened cryosparc_P105_J41_005_volume_map_sharp.mrc as #6, grid size 400,400,400, pixel 2.12, shown at level 0.211, step 2, values float32 > open /Users/z.kilic/Desktop/Chimeraimages/listed.cxs format session Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > open /Users/z.kilic/Desktop/Chimeraimages/TLE6_1.pdb format pdb Summary of feedback from opening /Users/z.kilic/Desktop/Chimeraimages/TLE6_1.pdb --- warnings | Start residue of secondary structure not found: HELIX 1 1 ASP A 97 PHE A 109 1 13 Start residue of secondary structure not found: HELIX 2 2 SER A 119 PHE A 129 1 11 Start residue of secondary structure not found: HELIX 3 3 GLY A 150 GLY A 165 1 16 Start residue of secondary structure not found: HELIX 4 4 ARG A 180 ILE A 182 1 3 Start residue of secondary structure not found: HELIX 5 5 SER A 189 CYS A 198 1 10 170 messages similar to the above omitted Chain information for TLE6_1.pdb #24 --- Chain | Description B | No description available > open /Users/z.kilic/Desktop/Chimeraimages/tuba1c_1.pdb format pdb tuba1c_1.pdb title: Alphafold monomer V2.0 prediction for tubulin α-1C chain (P68373) [more info...] Chain information for tuba1c_1.pdb #25 --- Chain | Description | UniProt A | tubulin α-1C chain | TBA1C_MOUSE 1-449 > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs format session Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > open /Users/z.kilic/Downloads/MmCPLs_fit-SCMC-PADI6_250529.cxs format > session Opened cryosparc_P105_J56_006_volume_map_sharp.mrc as #1, grid size 400,400,400, pixel 2.12, shown at level 0.289, step 1, values float32 Opened cryosparc_P105_J67_007_volume_map_sharp.mrc as #4, grid size 300,300,300, pixel 2.12, shown at level 0.276, step 1, values float32 opened ChimeraX session > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs format session Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > view front Expected an objects specifier or a view name or a keyword > view name front > view front > view name front > view front > hide #4-6,8-13,15,17-19,21-23#!3,7,14,16,20 target m > open /Users/z.kilic/Downloads/MmCPLs_playground.cxs Opened cryosparc_P105_J104_004_volume_map_deepEM_tight.mrc as #1, grid size 300,300,300, pixel 2.12, shown at level 0.0305, step 1, values float32 Opened MmCPLs_UNK4.mrc as #7, grid size 32,32,38, pixel 2.12,2.12,2.12, shown at level 0.159, step 1, values float32 Opened MmCPLs_UNK1.mrc as #16, grid size 32,32,32, pixel 2.12, shown at level 0.193, step 1, values float32 Opened MmCPLs_UNK2.mrc as #20, grid size 34,34,34, pixel 2.12, shown at level 0.226, step 1, values float32 opened ChimeraX session > view name front > select add #1 4 models selected > getcrd sel No atoms specified > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 6 models selected > getcrd sel Atom #2/A:97@N 461.906 406.838 408.908 [deleted to fit within ticket limits] #6/A:469@OXT color #d783ff > view front > show #!1 models > color #1 #b2b2b280 models Color zone shortcut requires 1 displayed atomic model and 1 map, got 14 atomic models, 1 maps. > select add #1 2 models selected Color zone shortcut requires 1 displayed atomic model and 1 map, got 14 atomic models, 1 maps. > select subtract #1 Nothing selected > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > select add #3 30130 atoms, 30707 bonds, 4 pseudobonds, 3803 residues, 3 models selected > select add #6 33934 atoms, 34606 bonds, 4 pseudobonds, 4272 residues, 4 models selected > select add #9 44710 atoms, 45628 bonds, 4 pseudobonds, 5636 residues, 5 models selected > select add #10 55486 atoms, 56650 bonds, 4 pseudobonds, 7000 residues, 6 models selected > select add #11 66262 atoms, 67672 bonds, 4 pseudobonds, 8364 residues, 7 models selected > select add #12 77038 atoms, 78694 bonds, 4 pseudobonds, 9728 residues, 8 models selected > select add #13 87814 atoms, 89716 bonds, 4 pseudobonds, 11092 residues, 9 models selected > select add #14 110005 atoms, 112337 bonds, 8 pseudobonds, 13902 residues, 11 models selected > select add #15 163885 atoms, 167447 bonds, 8 pseudobonds, 20722 residues, 12 models selected > select add #19 170792 atoms, 174516 bonds, 8 pseudobonds, 21592 residues, 13 models selected > select add #23 178731 atoms, 182602 bonds, 8 pseudobonds, 22585 residues, 14 models selected > select add #24 185638 atoms, 189671 bonds, 8 pseudobonds, 23455 residues, 15 models selected > color zone #1 near sel distance 5 > color zone #1 near sel distance 7 > color zone #1 near sel distance 5 > color zone #1 near sel distance 7 > color zone #1 near sel distance 5 > color zone #1 near sel distance 7 > transparency 50 > ~select Nothing selected > ui mousemode right clip > clip on Expected a keyword > clip back move 10 Invalid ""back"" argument: Expected 'off' or a number > clip back front move 10 Invalid ""back"" argument: Expected 'off' or a number > clip front move 10 Invalid ""front"" argument: Expected 'off' or a number > clip front move 10 Invalid ""front"" argument: Expected 'off' or a number > clip front 10 > clip front 1 > clip front -10 > clip front -5 > clip front -10 > clip front -15 > clip front -30 > clip front 5 > clip front -1 > clip front 1 > clip reset Expected a keyword > clip off > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > focus sel Unknown command: focus sel > focus #2 Unknown command: focus #2 > focus #2 Unknown command: focus #2 > focus atoms #2 Unknown command: focus atoms #2 > info version Expected a models specifier or a keyword > select subtract #2 Nothing selected > view > view front > lighting soft > lighting simple > lighting soft > lighting full > lighting soft > lighting full > lighting soft > lighting simple > lighting soft > lighting simple > lighting soft > graphics silhouettes false > lighting full > lighting soft > lighting simple > lighting soft > graphics silhouettes true > lighting soft > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > view sel > clip off > focus Unknown command: focus > view sel > lighting soft > ui mousemode right zone > ui mousemode right clip > ui mousemode right zone > ui mousemode right clip > ui tool show ""Side View"" > select subtract #2 Nothing selected > clip front -1 > clip off > clip 1 Expected a keyword > clip 1 Expected a keyword > clip 1 Expected a keyword > clip 1 Expected a keyword > clip 1 Expected a keyword > clip 1 Expected a keyword > clip 1 Expected a keyword > clip front 1 > clip off > clip front -5 > clip front 1 > clip front -5 > clip front 1 > clip back -1 > clip back 1 > save > /Users/z.kilic/Desktop/Chimeraimages/Zeynep_CPLplaygroundfigures/SCMC_upclose.png > width 2000 height 1479 supersample 4 > view > select add #2 22191 atoms, 22621 bonds, 4 pseudobonds, 2810 residues, 2 models selected > view sel > select subtract #2 Nothing selected > save > /Users/z.kilic/Desktop/Chimeraimages/Zeynep_CPLplaygroundfigures/SCMC_upclose.png > width 2000 height 1479 supersample 4 > clip front Missing ""front"" keyword's argument > clip front Missing ""front"" keyword's argument > clip front Missing ""front"" keyword's argument > clip front 5 > clip front -0,5 Invalid ""front"" argument: Expected 'off' or a number > clip front -0,5 Invalid ""front"" argument: Expected 'off' or a number > clip front -0.5 > clip front 0.2 > clip front -0.2 > save > /Users/z.kilic/Desktop/Chimeraimages/Zeynep_CPLplaygroundfigures/SCMC_upclose.png > width 2000 height 1479 supersample 4 > clip front -5 > clip front -10 > clip front -15 > front view Unknown command: front view > view front > save > /Users/z.kilic/Desktop/Chimeraimages/Zeynep_CPLplaygroundfigures/SCMC_upclose.png > width 2000 height 1479 supersample 4 > view front > clip off > transparency 20 > transparency 80 > transparency 60 > transparency 50 > transparency 60 > save > /Users/z.kilic/Desktop/Chimeraimages/Zeynep_CPLplaygroundfigures/frontviewtransparent.png > width 2000 height 1479 supersample 4 > ui mousemode right translate > hide #6 models > hide #19 models > hide #!2 models > hide #3 models > hide #!14 models > hide #15 models > show #15 models > hide #23 models > hide #24 models > hide #25 models > hide #9 models > hide #10 models > hide #11 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > show #12 models > show #11 models > show #10 models > show #9 models > show #!2 models > hide #13 models > hide #12 models > hide #11 models > hide #10 models > hide #9 models > hide #15 models > ui mousemode right clip > show #9 models > hide #9 models > show #9 models > hide #9 models > show #9 models > hide #9 models > show #9 models > hide #9 models > show #9 models > hide #9 models > show #9 models > hide #9 models > save > /Users/z.kilic/Desktop/Chimeraimages/Zeynep_CPLplaygroundfigures/SCMC_upclose.png > width 2000 height 1479 supersample 4 > hide #!2 models > show #9 models > show #10 models > show #11 models > show #12 models > show #13 models > clip bakc 5 Expected a keyword > clip back 5 > clip back -5 > hide #10 models > show #10 models > hide #12 models > show #12 models > hide #13 models > show #13 models > hide #9 models > show #9 models > hide #9 models > hide #10 models > hide #11 models > hide #12 models > hide #13 models > show #13 models > show #12 models > show #11 models > show #10 models > show #9 models > color #10 F3BAC3 Expected a color or one of 'byatom', 'bychain', 'byelement', 'byhetero', 'byidentity', 'bymodel', 'bynucleotide', 'bypolymer', 'fromatoms', 'fromcartoons', 'fromribbons', or 'random' or a keyword > color #10 #F3BAC3 > color #10 #EA8695 > color #12 #EA8695 > save > /Users/z.kilic/Desktop/Chimeraimages/Zeynep_CPLplaygroundfigures/PADI6_closeup.png > width 2000 height 1479 supersample 4 > hide #13 models > hide #12 models > show #12 models > hide #12 models > show #12 models > hide #12 models > hide #11 models > hide #10 models > show #10 models > hide #!1 models > show #11 models > hide #11 models > show #11 models > hide #11 models > show #11 models > hide #11 models > show #11 models > show #12 models > show #13 models > show #!14 models > hide #!14 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > hide #!1 models > show #!1 models > select add #13 10776 atoms, 11022 bonds, 1364 residues, 1 model selected > select add #12 21552 atoms, 22044 bonds, 2728 residues, 2 models selected > select add #11 32328 atoms, 33066 bonds, 4092 residues, 3 models selected > select add #10 43104 atoms, 44088 bonds, 5456 residues, 4 models selected > select add #9 53880 atoms, 55110 bonds, 6820 residues, 5 models selected > select add #2 76071 atoms, 77731 bonds, 4 pseudobonds, 9630 residues, 7 models selected > select add #19 82978 atoms, 84800 bonds, 4 pseudobonds, 10500 residues, 8 models selected > show #25 models > view front > hide #9 models > hide #10 models > hide #11 models > hide #12 models > show #12 models > show #11 models > show #10 models > show #9 models > select subtract #2 60787 atoms, 62179 bonds, 7690 residues, 6 models selected > select subtract #19 53880 atoms, 55110 bonds, 6820 residues, 5 models selected > hide #25 models > hide #!1 models > show #!1 models > select add #22 56347 atoms, 57635 bonds, 7133 residues, 6 models selected > select subtract #22 53880 atoms, 55110 bonds, 6820 residues, 5 models selected > clip off > view front > select add #25 57684 atoms, 59009 bonds, 7289 residues, 6 models selected > select subtract #25 53880 atoms, 55110 bonds, 6820 residues, 5 models selected > select add #22 56347 atoms, 57635 bonds, 7133 residues, 6 models selected > select subtract #22 53880 atoms, 55110 bonds, 6820 residues, 5 models selected > show #22 models > show #!2 models > show #25 models > show #!14 models > hide #!14 models > show #!14 models > hide #22 models > hide #25 models > hide #!2 models > select subtract #9 43104 atoms, 44088 bonds, 5456 residues, 4 models selected > select subtract #10 32328 atoms, 33066 bonds, 4092 residues, 3 models selected > select subtract #11 21552 atoms, 22044 bonds, 2728 residues, 2 models selected > select subtract #12 10776 atoms, 11022 bonds, 1364 residues, 1 model selected > select subtract #13 Nothing selected > hide #!1 models > show #!2 models > hide #!2 models > hide #!14 models > show #!1 models > hide #13 models > hide #12 models > hide #11 models > hide #10 models > hide #9 models > transparency 0 > view orient > ui mousemode right ""tape measure"" > marker segment #26 position 426.7,567,332.1 toPosition 573.1,426.8,332.1 > color yellow radius 0.53 label 202.8 labelHeight 20.28 labelColor yellow > marker segment #26 position 454.9,195,330 toPosition 183.2,439.2,333.6 color > yellow radius 0.53 label 365.4 labelHeight 36.54 labelColor yellow > marker segment #26 position 88.29,174.1,331.1 toPosition 451.6,545.1,363.9 > color yellow radius 0.53 label 520.3 labelHeight 52.03 labelColor yellow > marker segment #26 position 198.6,197.4,353.2 toPosition 431.9,439.1,359.5 > color yellow radius 0.53 label 336 labelHeight 33.6 labelColor yellow > marker segment #26 position 177,234.9,405.3 toPosition 403.6,459.2,286.5 > color yellow radius 0.53 label 340.3 labelHeight 34.03 labelColor yellow > ui mousemode right ""tape measure"" > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models > show #!26 models > hide #!26 models ===== Log before crash end ===== Log: Startup Messages --- note | available bundle cache has not been initialized yet UCSF ChimeraX version: 1.9 (2024-12-11) © 2016-2024 Regents of the University of California. All rights reserved. How to cite UCSF ChimeraX OpenGL version: 4.1 Metal - 89.4 OpenGL renderer: Apple M3 OpenGL vendor: Apple Python: 3.11.4 Locale: en_US.UTF-8 Qt version: PyQt6 6.7.1, Qt 6.7.1 Qt runtime version: 6.7.3 Qt platform: cocoa Hardware: Hardware Overview: Model Name: MacBook Air Model Identifier: Mac15,12 Model Number: Z1B8001YTN/A Chip: Apple M3 Total Number of Cores: 8 (4 performance and 4 efficiency) Memory: 16 GB System Firmware Version: 11881.101.1 OS Loader Version: 11881.101.1 Software: System Software Overview: System Version: macOS 15.4.1 (24E263) Kernel Version: Darwin 24.4.0 Time since boot: 7 days, 5 hours, 44 minutes Graphics/Displays: Apple M3: Chipset Model: Apple M3 Type: GPU Bus: Built-In Total Number of Cores: 10 Vendor: Apple (0x106b) Metal Support: Metal 3 Displays: Color LCD: Display Type: Built-in Liquid Retina Display Resolution: 2560 x 1664 Retina Main Display: Yes Mirror: Off Online: Yes Automatically Adjust Brightness: Yes Connection Type: Internal S24R65x: Resolution: 1920 x 1080 (1080p FHD - Full High Definition) UI Looks like: 1920 x 1080 @ 75.00Hz Mirror: Off Online: Yes Rotation: Supported Installed Packages: alabaster: 1.0.0 anyio: 4.7.0 appdirs: 1.4.4 appnope: 0.1.4 asttokens: 3.0.0 auditwheel: 6.1.0 babel: 2.16.0 beautifulsoup4: 4.12.3 blockdiag: 3.0.0 blosc2: 3.0.0 build: 1.2.1 certifi: 2023.11.17 cftime: 1.6.4.post1 charset-normalizer: 3.4.0 ChimeraX-AddCharge: 1.5.18 ChimeraX-AddH: 2.2.6 ChimeraX-AlignmentAlgorithms: 2.0.2 ChimeraX-AlignmentHdrs: 3.5 ChimeraX-AlignmentMatrices: 2.1 ChimeraX-Alignments: 2.16.1 ChimeraX-AlphaFold: 1.0.1 ChimeraX-AltlocExplorer: 1.1.2 ChimeraX-AmberInfo: 1.0 ChimeraX-Arrays: 1.1 ChimeraX-Atomic: 1.58.8 ChimeraX-AtomicLibrary: 14.1.11 ChimeraX-AtomSearch: 2.0.1 ChimeraX-AxesPlanes: 2.4 ChimeraX-BasicActions: 1.1.2 ChimeraX-BILD: 1.0 ChimeraX-BlastProtein: 3.0.0 ChimeraX-BondRot: 2.0.4 ChimeraX-BugReporter: 1.0.1 ChimeraX-BuildStructure: 2.13.1 ChimeraX-Bumps: 1.0 ChimeraX-BundleBuilder: 1.4.0 ChimeraX-ButtonPanel: 1.0.1 ChimeraX-CageBuilder: 1.0.1 ChimeraX-CellPack: 1.0 ChimeraX-Centroids: 1.4 ChimeraX-ChangeChains: 1.1 ChimeraX-CheckWaters: 1.4 ChimeraX-ChemGroup: 2.0.1 ChimeraX-Clashes: 2.3 ChimeraX-ColorActions: 1.0.5 ChimeraX-ColorGlobe: 1.0 ChimeraX-ColorKey: 1.5.6 ChimeraX-CommandLine: 1.2.5 ChimeraX-ConnectStructure: 2.0.1 ChimeraX-Contacts: 1.0.1 ChimeraX-Core: 1.9 ChimeraX-CoreFormats: 1.2 ChimeraX-coulombic: 1.4.4 ChimeraX-Crosslinks: 1.0 ChimeraX-Crystal: 1.0 ChimeraX-CrystalContacts: 1.0.1 ChimeraX-DataFormats: 1.2.3 ChimeraX-Dicom: 1.2.6 ChimeraX-DistMonitor: 1.4.2 ChimeraX-DockPrep: 1.1.3 ChimeraX-Dssp: 2.0 ChimeraX-EMDB-SFF: 1.0 ChimeraX-ESMFold: 1.0 ChimeraX-FileHistory: 1.0.1 ChimeraX-FunctionKey: 1.0.1 ChimeraX-Geometry: 1.3 ChimeraX-gltf: 1.0 ChimeraX-Graphics: 1.4.1 ChimeraX-Hbonds: 2.5 ChimeraX-Help: 1.3 ChimeraX-HKCage: 1.3 ChimeraX-IHM: 1.1 ChimeraX-ImageFormats: 1.2 ChimeraX-IMOD: 1.0 ChimeraX-IO: 1.0.3 ChimeraX-ItemsInspection: 1.0.1 ChimeraX-IUPAC: 1.0 ChimeraX-KVFinder: 1.2.1 ChimeraX-Label: 1.1.14 ChimeraX-ListInfo: 1.2.2 ChimeraX-Log: 1.2 ChimeraX-LookingGlass: 1.1 ChimeraX-Maestro: 1.9.1 ChimeraX-Map: 1.3 ChimeraX-MapData: 2.0 ChimeraX-MapEraser: 1.0.1 ChimeraX-MapFilter: 2.0.1 ChimeraX-MapFit: 2.0 ChimeraX-MapSeries: 2.1.1 ChimeraX-Markers: 1.0.1 ChimeraX-Mask: 1.0.2 ChimeraX-MatchMaker: 2.1.6 ChimeraX-MCopy: 1.0 ChimeraX-MDcrds: 2.7.2 ChimeraX-MedicalToolbar: 1.1 ChimeraX-Meeting: 1.0.1 ChimeraX-MLP: 1.1.1 ChimeraX-mmCIF: 2.14.2 ChimeraX-MMTF: 2.2 ChimeraX-ModelArchive: 1.0 ChimeraX-Modeller: 1.5.18 ChimeraX-ModelPanel: 1.5 ChimeraX-ModelSeries: 1.0.1 ChimeraX-Mol2: 2.0.3 ChimeraX-Mole: 1.0 ChimeraX-Morph: 1.0.2 ChimeraX-MouseModes: 1.2 ChimeraX-Movie: 1.0 ChimeraX-MutationScores: 1.0 ChimeraX-Neuron: 1.0 ChimeraX-Nifti: 1.2 ChimeraX-NMRSTAR: 1.0.2 ChimeraX-NRRD: 1.2 ChimeraX-Nucleotides: 2.0.3 ChimeraX-OpenCommand: 1.14 ChimeraX-OrthoPick: 1.0.1 ChimeraX-PDB: 2.7.6 ChimeraX-PDBBio: 1.0.1 ChimeraX-PDBLibrary: 1.0.4 ChimeraX-PDBMatrices: 1.0 ChimeraX-PickBlobs: 1.0.1 ChimeraX-Positions: 1.0 ChimeraX-PresetMgr: 1.1.2 ChimeraX-PubChem: 2.2 ChimeraX-ReadPbonds: 1.0.1 ChimeraX-Registration: 1.1.2 ChimeraX-RemoteControl: 1.0 ChimeraX-RenderByAttr: 1.6.2 ChimeraX-RenumberResidues: 1.1 ChimeraX-ResidueFit: 1.0.1 ChimeraX-RestServer: 1.3.1 ChimeraX-RNALayout: 1.0 ChimeraX-RotamerLibMgr: 4.0 ChimeraX-RotamerLibsDunbrack: 2.0 ChimeraX-RotamerLibsDynameomics: 2.0 ChimeraX-RotamerLibsRichardson: 2.0 ChimeraX-SaveCommand: 1.5.1 ChimeraX-SchemeMgr: 1.0 ChimeraX-SDF: 2.0.2 ChimeraX-Segger: 1.0 ChimeraX-Segment: 1.0.1 ChimeraX-Segmentations: 3.5.6 ChimeraX-SelInspector: 1.0 ChimeraX-SeqView: 2.14 ChimeraX-Shape: 1.0.1 ChimeraX-Shell: 1.0.1 ChimeraX-Shortcuts: 1.2.0 ChimeraX-ShowSequences: 1.0.3 ChimeraX-SideView: 1.0.1 ChimeraX-SimilarStructures: 1.0.1 ChimeraX-Smiles: 2.1.2 ChimeraX-SmoothLines: 1.0 ChimeraX-SpaceNavigator: 1.0 ChimeraX-StdCommands: 1.18.1 ChimeraX-STL: 1.0.1 ChimeraX-Storm: 1.0 ChimeraX-StructMeasure: 1.2.1 ChimeraX-Struts: 1.0.1 ChimeraX-Surface: 1.0.1 ChimeraX-SwapAA: 2.0.1 ChimeraX-SwapRes: 2.5 ChimeraX-TapeMeasure: 1.0 ChimeraX-TaskManager: 1.0 ChimeraX-Test: 1.0 ChimeraX-Toolbar: 1.2.3 ChimeraX-ToolshedUtils: 1.2.4 ChimeraX-Topography: 1.0 ChimeraX-ToQuest: 1.0 ChimeraX-Tug: 1.0.1 ChimeraX-UI: 1.41 ChimeraX-Umap: 1.0 ChimeraX-uniprot: 2.3.1 ChimeraX-UnitCell: 1.0.1 ChimeraX-ViewDockX: 1.4.4 ChimeraX-VIPERdb: 1.0 ChimeraX-Vive: 1.1 ChimeraX-VolumeMenu: 1.0.1 ChimeraX-vrml: 1.0 ChimeraX-VTK: 1.0 ChimeraX-WavefrontOBJ: 1.0 ChimeraX-WebCam: 1.0.2 ChimeraX-WebServices: 1.1.4 ChimeraX-Zone: 1.0.1 colorama: 0.4.6 comm: 0.2.2 contourpy: 1.3.1 cxservices: 1.2.3 cycler: 0.12.1 Cython: 3.0.10 debugpy: 1.8.9 decorator: 5.1.1 docutils: 0.21.2 executing: 2.1.0 filelock: 3.15.4 fonttools: 4.55.3 funcparserlib: 2.0.0a0 glfw: 2.8.0 grako: 3.16.5 h11: 0.14.0 h5py: 3.12.1 html2text: 2024.2.26 httpcore: 1.0.7 httpx: 0.28.1 idna: 3.10 ihm: 1.3 imagecodecs: 2024.6.1 imagesize: 1.4.1 ipykernel: 6.29.5 ipython: 8.26.0 ipywidgets: 8.1.5 jedi: 0.19.1 Jinja2: 3.1.4 jupyter_client: 8.6.2 jupyter_core: 5.7.2 jupyterlab_widgets: 3.0.13 kiwisolver: 1.4.7 line_profiler: 4.1.3 lxml: 5.2.2 lz4: 4.3.3 MarkupSafe: 3.0.2 matplotlib: 3.9.2 matplotlib-inline: 0.1.7 msgpack: 1.0.8 ndindex: 1.9.2 nest-asyncio: 1.6.0 netCDF4: 1.6.5 networkx: 3.3 nibabel: 5.2.0 nptyping: 2.5.0 numexpr: 2.10.2 numpy: 1.26.4 openvr: 1.26.701 packaging: 23.2 ParmEd: 4.2.2 parso: 0.8.4 pep517: 0.13.1 pexpect: 4.9.0 pillow: 10.4.0 pip: 24.2 pkginfo: 1.11.1 platformdirs: 4.3.6 prompt_toolkit: 3.0.48 psutil: 6.0.0 ptyprocess: 0.7.0 pure_eval: 0.2.3 py-cpuinfo: 9.0.0 pycollada: 0.8 pydicom: 2.4.4 pyelftools: 0.31 Pygments: 2.18.0 pynmrstar: 3.3.4 pynrrd: 1.0.0 PyOpenGL: 3.1.7 PyOpenGL-accelerate: 3.1.7 pyopenxr: 1.0.3401 pyparsing: 3.2.0 pyproject_hooks: 1.2.0 PyQt6-commercial: 6.7.1 PyQt6-Qt6: 6.7.3 PyQt6-WebEngine-commercial: 6.7.0 PyQt6-WebEngine-Qt6: 6.7.3 PyQt6-WebEngineSubwheel-Qt6: 6.7.3 PyQt6_sip: 13.8.0 python-dateutil: 2.9.0.post0 pytz: 2024.2 pyzmq: 26.2.0 qtconsole: 5.5.2 QtPy: 2.4.2 qtshim: 1.0 RandomWords: 0.4.0 requests: 2.32.3 scipy: 1.14.0 setuptools: 72.1.0 sfftk-rw: 0.8.1 six: 1.16.0 sniffio: 1.3.1 snowballstemmer: 2.2.0 sortedcontainers: 2.4.0 soupsieve: 2.6 Sphinx: 8.0.2 sphinx-autodoc-typehints: 2.2.3 sphinxcontrib-applehelp: 2.0.0 sphinxcontrib-blockdiag: 3.0.0 sphinxcontrib-devhelp: 2.0.0 sphinxcontrib-htmlhelp: 2.1.0 sphinxcontrib-jsmath: 1.0.1 sphinxcontrib-qthelp: 2.0.0 sphinxcontrib-serializinghtml: 2.0.0 stack-data: 0.6.3 superqt: 0.6.3 tables: 3.10.1 tcia_utils: 1.5.1 tifffile: 2024.7.24 tinyarray: 1.2.4 tornado: 6.4.2 traitlets: 5.14.3 typing_extensions: 4.12.2 tzdata: 2024.2 urllib3: 2.2.3 wcwidth: 0.2.13 webcolors: 24.6.0 wheel: 0.43.0 wheel-filename: 1.4.1 widgetsnbextension: 4.0.13 }}} " defect closed normal Window Toolkit duplicate all ChimeraX